ASSESSMENT OF GENETIC DIVERSITY IN TINOSPORA CORDIFOLIA BY INTER SIMPLE SEQUENCE REPEATS (ISSR) AND EXPRESSED SEQUENCE TAGGED- SIMPLE SEQUENCE REPEATS (EST-SSR)

Authors

  • Khusboo Singh Department of Genetics, M.D. University, Rohtak-124001, Haryana, India
  • Sangeeta Kadyan Department of Genetics, M.D. University, Rohtak-124001, Haryana, India
  • Manju Panghal Department of Genetics, M.D. University, Rohtak-124001, Haryana, India
  • Jaya Parkash Yadav Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Keywords:

Tinospora cordifolia, ISSR, EST-SSR, Genetic diversity

Abstract

Objective: In this study, assessment of genetic diversity was carried out using two kinds of molecular markers: Inter-Simple Sequence Repeats (ISSR) and Expressed Sequence Tag Simple Sequence Repeats (EST-SSR) in T. cordifolia.

Methods: A total of 20 primers/primer pairs were tested for the detection of polymorphism. For genetic diversity assessment, certain parameters such as Polymorphic Information Content (PIC), Marker Index (MI), effective multiplex ratio (EMR) and DDI (Diversity detecting Index) were used.

Results: The PIC, MI, EMR and DDI values ranges from 0.306-0.351, 0.76-1.18, 3.86-2.16 and 0.739-0.175 respectively. Cluster analysis based on Jaccard`s similarity coefficient using an Unweighted Pair Group Method with Arithmetic mean (UPGMA) classified all 24 accessions in to two major clusters respectively for both the marker system which demarcated the accessions according to different climatic zones. Similarity indices ranged from 0.68-1.0 for ISSR and 0.52-0.96 for EST-SSR.

Conclusion: Both marker systems ISSR and EST-SSR separate out the accessions from different climatic zones in to different groups. In addition, both have shown a high genetic diversity and a good consistency among different genotypes of T. cordifolia. Out of these two, EST-SSR proves more efficient as it directly correlates with the geographical distribution of the plant.

Downloads

Download data is not yet available.

Author Biographies

Khusboo Singh, Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Resaerch Scholar

Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Sangeeta Kadyan, Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Resaerch Scholar

Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Manju Panghal, Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Jaya Parkash Yadav, Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

Profeesor

Department of Genetics, M.D. University, Rohtak-124001, Haryana, India

References

Sun M. Effects of population size, mating system and evolutionary origin on genetic diversity in Spiranthes sinensis and S. hongkongensis. Cons Bio 1996;10:10785-95.

Tuskan GA, Gunter LE, Yang ZK, Yin TM, Sewell MM, Di-Fazio SP. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J For Res 2004;34:85-93.

Yin TM, DiFazio SP, Gunter LE, Zhang XY, Sewell MM, Woolbright SA, et al. Genome structure and emerging evidence of an incipient sex chromosome in Populus. Gen Res 2008;18:422-30.

Barth S, Melchinger AE, Lubberstedt TH. Genetic diversity in Arabidopsis thaliana L. Henyh. Investigated by cleaved amplified polymorphic sequence (CAPS) and inter simple sequence repeats (ISSR) markers. Mol Ecol 2002;11:495-505.

Huang CQ, Liu GD, Bai CJ, Wang WQ, Zhou SY, Yu DQ. Estimation of genetic variation in Cynodon dactylon accessions using the ISSR technique. Biochem Sys Ecol 2010;38:463-70.

Pashley CH, Ellis JR, McCauley DE, Burke JM. EST databases as a source for molecular markers: lessons from Helianthus. J Hered 2006;97:381-8.

Becher R. EST-derived microsatellites as a rich source of molecular markers for oats. Pl Breed 2007;126:274-8.

Heesacker A, Kishore VK, Gao WX, Tang SX, Kolkman JM, Gingle A, et al. SSRs and INDELs mined from the sun-Xower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 2008;117:1021-9.

Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, et al. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Gen 2008;9:287.

Mulato BM, Möller M, Zucchi MI, Quecini V, Pinheiro JB. Genetic diversity in soybean germplasm identified by SSR and EST-SSR markers. Pesq Agrop Brasil 2010;45:276-83.

Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W. Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Not 2010;3:42.

Ramu P, Billot C, Rami JF, Senthilvel S, Upadhyaya HD, Reddy LA, et al. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor Appl Genet 2013;126:2051-64.

Ahmad SM, Hoot SB, Qazi PH, Verma V. Phylogenetic patterns and genetic diversity of Indian Tinospora species based on chloroplast sequence data and cytochrome P450 polymorphisms. Pl Syst Evol 2009;281:87-96.

Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987;19:11-5.

Temnykh S, Lukashova A, Cartinhour S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Gen Res 2001;11:1441-52.

Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucl Aci Res 2012;40:e115.

Rohlf FJ NTSYS-pc 2.0e. Exeter Software, Setauket, New York, USA; 1998.

Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, et al. An evaluation of the utility of SSR loci as molecular marker in maize (Zea mays L.): comparison with data from RFLPS and pedigree. Theor Appl Genet 1997;95:163-73.

Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, et al. The comparison of RFPL, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 1996;2:225-38.

Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, et al. Comparison of PCR-based marker system for analysis of genetic relationship in cultivated potato. Mol Breed 1997;3:127-36.

Rout GR. Identiï¬cation of Tinospora cordifolia (Willd.) Miers ex Hook. F. and Thoms using RAPD markers. J Biosci 2006;61:118-22.

Shinde VM, Dhalwal K. DNA ï¬ngerprinting of Tinospora cordifolia using RAPD analysis. J Glob Pharm Tech 2012;2:38–42.

Rana V, Thakur K, Sood R, Sharma V, Sharma TR. Genetic diversity analysis of Tinospora cordifolia germplasm collected from northwestern Himalayan region of India. J Genet 2012;91:99-103.

Deshwal RPS, Singh R, Malik K, Randhawa GJ. Assessment of genetic diversity and genetic relationships among 29 populations of Azadirachta indica A. Juss using RAPD markers. Genet Res Cr Evol 2005;52:285-92.

Singh A, Negi MS, Rajagopal J, Bhatia S. Assessment of genetic diversity in Azadirachta indica using AFLP markers. Theoret Appl Genet 1999;99:272-9.

Sangwan RS, Sangwan NS, Jain DC, Kumar S, Ranade AS. RAPD profile based genetic characterization of chemotypic variants of Artemisia annua L. Biochem Mol Bio Int 1999;47:935-44.

Keskitalo M, Pehu E, Simon JE. Variation in volatile compounds from tansy (Tanacetum vulgare L.) related to genetic and morphological differences of genotypes. Biochem Syst Ecol 2001;29:267-85.

Farajpour M, Ebrahimi M, Amiri R, Sadat-Noori SH, Sanjari S, et al. Study of genetic variation in yarrow using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers. Afr J Biotechnol 2011;54:11137-41.

Farajpour M, Ebrahimi M, Amiri R, Golzari R, Sanjari S. Assessment of genetic diversity in Achillea millefolium accessions from Iran using ISSR marker. Bioch Syst Ecol 2012;43:73-9.

Published

01-10-2014

How to Cite

Singh, K., S. Kadyan, M. Panghal, and J. P. Yadav. “ASSESSMENT OF GENETIC DIVERSITY IN TINOSPORA CORDIFOLIA BY INTER SIMPLE SEQUENCE REPEATS (ISSR) AND EXPRESSED SEQUENCE TAGGED- SIMPLE SEQUENCE REPEATS (EST-SSR)”. International Journal of Pharmacy and Pharmaceutical Sciences, vol. 6, no. 10, Oct. 2014, pp. 520-4, https://journals.innovareacademics.in/index.php/ijpps/article/view/2999.

Issue

Section

Original Article(s)